General information for g5884.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Very long-chain-fatty-acid–CoA ligase bubblegum.
Parent gene
- The parent gene g5884 is located on chr_2: 12584453..12586568 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g5884 | g5884.t5 | TSS | g5884.t5 | 12579796 | 12579796 |
| chr_2 | g5884 | g5884.t5 | isoform | g5884.t5 | 12579976 | 12584365 |
| chr_2 | g5884 | g5884.t5 | exon | g5884.t5.exon1 | 12579976 | 12579981 |
| chr_2 | g5884 | g5884.t5 | exon | g5884.t5.exon2 | 12583062 | 12583476 |
| chr_2 | g5884 | g5884.t5 | cds | g5884.t5.CDS1 | 12583124 | 12583476 |
| chr_2 | g5884 | g5884.t5 | exon | g5884.t5.exon3 | 12583546 | 12584365 |
| chr_2 | g5884 | g5884.t5 | cds | g5884.t5.CDS2 | 12583546 | 12584365 |
| chr_2 | g5884 | g5884.t5 | TTS | g5884.t5 | NA | NA |
Sequences
>g5884.t5 Gene=g5884 Length=1241
TGATTGATATATATTGAAAAATTAGTGACTTTTCTGCGTAATATAATTAAACAAAAAAAT
TAAACAACATGGCAAAACACGTTGCATTACGCGAAACGAAAGAATTTCGCATAACAGATC
CATCAAAACCCGTGAGAATATTTCAAAATCCACGTGATAAAACAGCATCGGTCGATCCTA
TTACAGTTCCAGCTCTCATGAATCGTACAGTAGAAAATTATGGTAATCATCCAGCTCTCA
AATACAAAGATCCTGTCACAGGAAAGTGGCAGACAATTACTTATAAAGAATACAAAGAAC
GCGTTGAGAAGATGGCTAAAGTTTTCATAAAACTTGGTCTCGAACGCTATGGCACTGTCG
CAGTTCTCGCATTCAATAGTGTTGAATGGTTTGTCTCTGAATTAGCGGCAATTCATGCCG
GTGGAAATATTGCTGGTGTATACACAACAAATTCTGTCGATTCAGTGTTTTATGTACTTG
ATAGTTGTAAAGCAAATATTGTCGTTGTTGATGATGCTAAACAAATGGAAAAGATTCATG
CAATTAAAGACAAATTGCCTCATTTAAAGGCCATCATTCAAACAATTTCACCTTATGCAC
CTTATGTTAAACGTGCTGATGGTTATTGGCGATGGAGTGAACTCCAAGAAATGAAGACTG
ATGATGTCGAAGAAGAATATCAGCGAAGACTCAAGAGTATAGTTGCAAACGAATGCTGTT
GTTTAGTTTATACATCAGGCACAACAGGCACACCAAAAGGTGCAATGTTATCGCACGATA
ATTTTACATGGGATGCTTACAGTTTCACAGTTTATGTGGATAATTTACAAATGGGAAAGG
AAGTTATAGTTAGTTATCTTCCACTTTCACATGTTGCTGCACAGATTATTGATATTTTCA
TTTCAATGACAATTGCTGCTACTGTATATTTTGCTGATAAAGATACATTAAAAGGATCAC
TCGTCAAAACACTCATTGATGCACGACCAACAAATTTTTTGGGTGTTCCACGTGTTTATG
AAAAAATTCAAGAAAAAATGATGGCTATTGGATCACAGTCGGGTGCATTAAAAAGAGCAA
TTGCATCATGGGCAAAAAGTGCAACATTAAAACATCATATGGAGAAAATGGCTGGTCGAC
CTTCAGCATCTTTGCAATACAAATTAGCAAATAAGATTGTAATGAGCAAAGTTAAGCAAG
CACTTGGTCTTAATCGATGCAAAAACTTTATCACTGGTGCA
>g5884.t5 Gene=g5884 Length=391
MAKHVALRETKEFRITDPSKPVRIFQNPRDKTASVDPITVPALMNRTVENYGNHPALKYK
DPVTGKWQTITYKEYKERVEKMAKVFIKLGLERYGTVAVLAFNSVEWFVSELAAIHAGGN
IAGVYTTNSVDSVFYVLDSCKANIVVVDDAKQMEKIHAIKDKLPHLKAIIQTISPYAPYV
KRADGYWRWSELQEMKTDDVEEEYQRRLKSIVANECCCLVYTSGTTGTPKGAMLSHDNFT
WDAYSFTVYVDNLQMGKEVIVSYLPLSHVAAQIIDIFISMTIAATVYFADKDTLKGSLVK
TLIDARPTNFLGVPRVYEKIQEKMMAIGSQSGALKRAIASWAKSATLKHHMEKMAGRPSA
SLQYKLANKIVMSKVKQALGLNRCKNFITGA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5884.t5 | Gene3D | G3DSA:3.40.50.12780 | - | 33 | 362 | 1.4E-51 |
| 2 | g5884.t5 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 9 | 391 | 1.8E-127 |
| 3 | g5884.t5 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 9 | 391 | 1.8E-127 |
| 1 | g5884.t5 | Pfam | PF00501 | AMP-binding enzyme | 46 | 338 | 8.7E-56 |
| 5 | g5884.t5 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 219 | 230 | - |
| 4 | g5884.t5 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 35 | 338 | 2.75E-55 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5884/g5884.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5884.t5.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed